diff mafft/core/Lalignmm.c @ 18:e4d75f9efb90 draft

planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mafft/core/Lalignmm.c	Thu Feb 02 18:44:31 2017 -0500
@@ -0,0 +1,2563 @@
+#include "mltaln.h"
+#include "dp.h"
+
+#define MEMSAVE 1
+
+#define DEBUG 0
+#define USE_PENALTY_EX  0
+#define STOREWM 1
+
+#define DPTANNI 10
+
+#define LOCAL 0
+
+static int reccycle = 0;
+
+static float localthr;
+
+static void match_ribosum( float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize )
+{
+	int j, k, l;
+	float scarr[38];
+	float **cpmxpd = floatwork;
+	int **cpmxpdn = intwork;
+	int count = 0;
+	float *matchpt;
+	float **cpmxpdpt;
+	int **cpmxpdnpt;
+	int cpkd;
+
+	if( initialize )
+	{
+		for( j=0; j<lgth2; j++ )
+		{
+			count = 0;
+			for( l=0; l<37; l++ )
+			{
+				if( cpmx2[j][l] )
+				{
+					cpmxpd[j][count] = cpmx2[j][l];
+					cpmxpdn[j][count] = l;
+					count++;
+				}
+			}
+			cpmxpdn[j][count] = -1;
+		}
+	}
+
+	for( l=0; l<37; l++ )
+	{
+		scarr[l] = 0.0;
+		for( k=0; k<37; k++ )
+		{
+			scarr[l] += ribosumdis[k][l] * cpmx1[i1][k];
+		}
+	}
+#if 0 /* これを使うときはfloatworkのアロケートを逆にする */
+	{
+		float *fpt, **fptpt, *fpt2;
+		int *ipt, **iptpt;
+		fpt2 = match;
+		iptpt = cpmxpdn;
+		fptpt = cpmxpd;
+		while( lgth2-- )
+		{
+			*fpt2 = 0.0;
+			ipt=*iptpt,fpt=*fptpt;
+			while( *ipt > -1 )
+				*fpt2 += scarr[*ipt++] * *fpt++;
+			fpt2++,iptpt++,fptpt++;
+		} 
+	}
+	for( j=0; j<lgth2; j++ )
+	{
+		match[j] = 0.0;
+		for( k=0; cpmxpdn[j][k]>-1; k++ )
+			match[j] += scarr[cpmxpdn[j][k]] * cpmxpd[j][k];
+	} 
+#else
+	matchpt = match;
+	cpmxpdnpt = cpmxpdn;
+	cpmxpdpt = cpmxpd;
+	while( lgth2-- )
+	{
+		*matchpt = 0.0;
+		for( k=0; (cpkd=(*cpmxpdnpt)[k])>-1; k++ )
+			*matchpt += scarr[cpkd] * (*cpmxpdpt)[k];
+		matchpt++;
+		cpmxpdnpt++;
+		cpmxpdpt++;
+	}
+#endif
+}
+
+static void match_calc( float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize )
+{
+	int j, k, l;
+//	float scarr[26];
+	float **cpmxpd = floatwork;
+	int **cpmxpdn = intwork;
+	int count = 0;
+	float *matchpt;
+	float **cpmxpdpt;
+	int **cpmxpdnpt;
+	int cpkd;
+	float *scarr;
+	scarr = calloc( nalphabets, sizeof( float ) );
+
+	if( initialize )
+	{
+		for( j=0; j<lgth2; j++ )
+		{
+			count = 0;
+			for( l=0; l<nalphabets; l++ )
+			{
+				if( cpmx2[j][l] )
+				{
+					cpmxpd[j][count] = cpmx2[j][l];
+					cpmxpdn[j][count] = l;
+					count++;
+				}
+			}
+			cpmxpdn[j][count] = -1;
+		}
+	}
+
+	for( l=0; l<nalphabets; l++ )
+	{
+		scarr[l] = 0.0;
+		for( k=0; k<nalphabets; k++ )
+		{
+			scarr[l] += (n_dis[k][l]-RNAthr) * cpmx1[i1][k];
+		}
+	}
+#if 0 /* これを使うときはfloatworkのアロケートを逆にする */
+	{
+		float *fpt, **fptpt, *fpt2;
+		int *ipt, **iptpt;
+		fpt2 = match;
+		iptpt = cpmxpdn;
+		fptpt = cpmxpd;
+		while( lgth2-- )
+		{
+			*fpt2 = 0.0;
+			ipt=*iptpt,fpt=*fptpt;
+			while( *ipt > -1 )
+				*fpt2 += scarr[*ipt++] * *fpt++;
+			fpt2++,iptpt++,fptpt++;
+		} 
+	}
+	for( j=0; j<lgth2; j++ )
+	{
+		match[j] = 0.0;
+		for( k=0; cpmxpdn[j][k]>-1; k++ )
+			match[j] += scarr[cpmxpdn[j][k]] * cpmxpd[j][k];
+	} 
+#else
+	matchpt = match;
+	cpmxpdnpt = cpmxpdn;
+	cpmxpdpt = cpmxpd;
+	while( lgth2-- )
+	{
+		*matchpt = 0.0;
+		for( k=0; (cpkd=(*cpmxpdnpt)[k])>-1; k++ )
+			*matchpt += scarr[cpkd] * (*cpmxpdpt)[k];
+		matchpt++;
+		cpmxpdnpt++;
+		cpmxpdpt++;
+	}
+#endif
+	free( scarr );
+}
+
+#if 0
+static void match_add( float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize )
+{
+	int j, k, l;
+	float scarr[nalphabets];
+	float **cpmxpd = floatwork;
+	int **cpmxpdn = intwork;
+	int count = 0;
+	float *matchpt;
+	float **cpmxpdpt;
+	int **cpmxpdnpt;
+	int cpkd;
+
+
+	if( initialize )
+	{
+		for( j=0; j<lgth2; j++ )
+		{
+			count = 0;
+			for( l=0; l<nalphabets; l++ )
+			{
+				if( cpmx2[j][l] )
+				{
+					cpmxpd[j][count] = cpmx2[j][l];
+					cpmxpdn[j][count] = l;
+					count++;
+				}
+			}
+			cpmxpdn[j][count] = -1;
+		}
+	}
+
+	for( l=0; l<nalphabets; l++ )
+	{
+		scarr[l] = 0.0;
+		for( k=0; k<nalphabets; k++ )
+		{
+			scarr[l] += n_dis[k][l] * cpmx1[i1][k];
+		}
+	}
+#if 0 /* これを使うときはfloatworkのアロケートを逆にする */
+	{
+		float *fpt, **fptpt, *fpt2;
+		int *ipt, **iptpt;
+		fpt2 = match;
+		iptpt = cpmxpdn;
+		fptpt = cpmxpd;
+		while( lgth2-- )
+		{
+			*fpt2 = 0.0;
+			ipt=*iptpt,fpt=*fptpt;
+			while( *ipt > -1 )
+				*fpt2 += scarr[*ipt++] * *fpt++;
+			fpt2++,iptpt++,fptpt++;
+		} 
+	}
+	for( j=0; j<lgth2; j++ )
+	{
+		match[j] = 0.0;
+		for( k=0; cpmxpdn[j][k]>-1; k++ )
+			match[j] += scarr[cpmxpdn[j][k]] * cpmxpd[j][k];
+	} 
+#else
+	matchpt = match;
+	cpmxpdnpt = cpmxpdn;
+	cpmxpdpt = cpmxpd;
+	while( lgth2-- )
+	{
+//		*matchpt = 0.0; // add dakara
+		for( k=0; (cpkd=(*cpmxpdnpt)[k])>-1; k++ )
+			*matchpt += scarr[cpkd] * (*cpmxpdpt)[k];
+		matchpt++;
+		cpmxpdnpt++;
+		cpmxpdpt++;
+	}
+#endif
+}
+#endif
+
+#if 0
+static float Atracking( 
+						char **seq1, char **seq2, 
+                        char **mseq1, char **mseq2, 
+                        int **ijp, int icyc, int jcyc,
+						int ist, int ien, int jst, int jen )
+{
+	int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k, klim;
+	char *gaptable1, *gt1bk;
+	char *gaptable2, *gt2bk;
+	lgth1 = ien-ist+1;
+	lgth2 = jen-jst+1;
+
+	gt1bk = AllocateCharVec( lgth1+lgth2+1 );
+	gt2bk = AllocateCharVec( lgth1+lgth2+1 );
+
+#if 0
+	for( i=0; i<lgth1; i++ ) 
+	{
+		fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
+	}
+#endif
+
+
+//	fprintf( stderr, "in Atracking, lgth1=%d, lgth2=%d\n", lgth1, lgth2 );
+ 
+    for( i=0; i<lgth1+1; i++ ) 
+    {
+        ijp[i][0] = i + 1;
+    }
+    for( j=0; j<lgth2+1; j++ ) 
+    {
+        ijp[0][j] = -( j + 1 );
+    }
+
+
+	gaptable1 = gt1bk + lgth1+lgth2;
+	*gaptable1 = 0;
+	gaptable2 = gt2bk + lgth1+lgth2;
+	*gaptable2 = 0;
+
+//	if( lgth2 == 1 ) fprintf( stderr, "in Atracking, mseq1 = %s, mseq2 = %s\n", mseq1[0], mseq2[0] );
+
+	iin = lgth1; jin = lgth2;
+	klim = lgth1+lgth2;
+	for( k=0; k<=klim; k++ ) 
+	{
+		if( ijp[iin][jin] < 0 ) 
+		{
+			ifi = iin-1; jfi = jin+ijp[iin][jin];
+		}
+		else if( ijp[iin][jin] > 0 )
+		{
+			ifi = iin-ijp[iin][jin]; jfi = jin-1;
+		}
+		else
+		{
+			ifi = iin-1; jfi = jin-1;
+		}
+		l = iin - ifi;
+		while( --l ) 
+		{
+			*--gaptable1 = 'o';
+			*--gaptable2 = '-';
+			k++;
+		}
+		l= jin - jfi;
+		while( --l )
+		{
+			*--gaptable1 = '-';
+			*--gaptable2 = 'o';
+			k++;
+		}
+		if( iin <= 0 || jin <= 0 ) break;
+		*--gaptable1 = 'o';
+		*--gaptable2 = 'o';
+		k++;
+		iin = ifi; jin = jfi;
+
+	}
+
+	for( i=0; i<icyc; i++ ) gapireru( mseq1[i], seq1[i]+ist, gaptable1 );
+	for( j=0; j<jcyc; j++ ) gapireru( mseq2[j], seq2[j]+jst, gaptable2 );
+
+	free( gt1bk );
+	free( gt2bk );
+
+//	fprintf( stderr, "in Atracking (owari), mseq1 = %s\n", mseq1[0] );
+//	fprintf( stderr, "in Atracking (owari), mseq2 = %s\n", mseq2[0] );
+	return( 0.0 );
+}
+#endif
+
+
+static float MSalign2m2m_rec( int icyc, int jcyc, double *eff1, double *eff2, char **seq1, char **seq2, float **cpmx1, float **cpmx2, int ist, int ien, int jst, int jen, int alloclen, char **mseq1, char **mseq2, int depth, float **gapinfo, float **map )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+	float value = 0.0;
+	register int i, j;
+	char **aseq1, **aseq2;
+	int ll1, ll2;
+	int lasti, lastj, imid, jmid = 0;
+	float wm = 0.0;   /* int ?????? */
+	float g;
+	float *currentw, *previousw;
+#if USE_PENALTY_EX
+	float fpenalty_ex = (float)penalty_ex;
+#endif
+//	float fpenalty = (float)penalty;
+	float *wtmp;
+//	short *ijppt;
+	int *mpjpt;
+//	short **ijp;
+	int *mp;
+	int mpi;
+	float *mjpt, *prept, *curpt;
+	float mi;
+	float *m;
+	float *w1, *w2;
+//	float *match;
+	float *initverticalw;    /* kufuu sureba iranai */
+	float *lastverticalw;    /* kufuu sureba iranai */
+	int **intwork;
+	float **floatwork;
+//	short **shortmtx;
+#if STOREWM
+	float **WMMTX;
+	float **WMMTX2;
+#endif
+	float *midw;
+	float *midm;
+	float *midn;
+	int lgth1, lgth2;
+	float maxwm = 0.0;
+	int *jumpforwi;
+	int *jumpforwj;
+	int *jumpbacki;
+	int *jumpbackj;
+	int *jumpdummi; //muda
+	int *jumpdummj; //muda
+	int jumpi, jumpj = 0;
+	char *gaps;
+	int ijpi, ijpj;
+	float *ogcp1;
+	float *fgcp1;
+	float *ogcp2;
+	float *fgcp2;
+	float firstm;
+	int firstmp;
+#if 0
+	static char ttt1[50000];
+	static char ttt2[50000];
+#endif
+
+	localthr = -offset + 500; // 0?
+
+	ogcp1 = gapinfo[0] + ist;
+	fgcp1 = gapinfo[1] + ist;
+	ogcp2 = gapinfo[2] + jst;
+	fgcp2 = gapinfo[3] + jst;
+
+	depth++;
+	reccycle++;
+
+	lgth1 = ien-ist+1;
+	lgth2 = jen-jst+1;
+
+//	if( lgth1 < 5 )
+//		fprintf( stderr, "\nWARNING: lgth1 = %d\n", lgth1 );
+//	if( lgth2 < 5 )
+//		fprintf( stderr, "\nWARNING: lgth2 = %d\n", lgth2 );
+//
+
+#if 0
+	fprintf( stderr, "==== MSalign (depth=%d, reccycle=%d), ist=%d, ien=%d, jst=%d, jen=%d\n", depth, reccycle, ist, ien, jst, jen );
+	strncpy( ttt1, seq1[0]+ist, lgth1 );
+	strncpy( ttt2, seq2[0]+jst, lgth2 );
+	ttt1[lgth1] = 0;
+	ttt2[lgth2] = 0;
+	fprintf( stderr, "seq1 = %s\n", ttt1 );
+	fprintf( stderr, "seq2 = %s\n", ttt2 );
+#endif
+	if( lgth2 <= 0 ) // lgth1 <= 0 ha?
+	{
+//		fprintf( stderr, "\n\n==== jimei\n\n" );
+//		exit( 1 );
+		for( i=0; i<icyc; i++ ) 
+		{
+			strncpy( mseq1[i], seq1[i]+ist, lgth1 );
+			mseq1[i][lgth1] = 0;
+		}
+		for( i=0; i<jcyc; i++ ) 
+		{
+			mseq2[i][0] = 0;
+			for( j=0; j<lgth1; j++ )
+				strcat( mseq2[i], "-" );
+		}
+
+//		fprintf( stderr, "==== mseq1[0] (%d) = %s\n", depth, mseq1[0] );
+//		fprintf( stderr, "==== mseq2[0] (%d) = %s\n", depth, mseq2[0] );
+
+		return( 0.0 );
+	}
+
+#if MEMSAVE
+	aseq1 = AllocateCharMtx( icyc, 0 );
+	aseq2 = AllocateCharMtx( jcyc, 0 );
+	for( i=0; i<icyc; i++ ) aseq1[i] = mseq1[i];
+	for( i=0; i<jcyc; i++ ) aseq2[i] = mseq2[i];
+#else
+	aseq1 = AllocateCharMtx( icyc, lgth1+lgth2+100 );
+	aseq2 = AllocateCharMtx( jcyc, lgth1+lgth2+100 );
+#endif
+
+//  if( lgth1 < DPTANNI && lgth2 < DPTANNI ) // & dato lgth ==1 no kanousei ga arunode yokunai 
+//    if( lgth1 < DPTANNI ) // kore mo lgth2 ga mijikasugiru kanousei ari
+    if( lgth1 < DPTANNI || lgth2 < DPTANNI ) // zettai ni anzen ka?
+	{
+//		fprintf( stderr, "==== Going to _tanni\n" );
+
+//		value = MSalignmm_tanni( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist, ien, jst, jen, alloclen, aseq1, aseq2, gapinfo );	
+
+
+#if MEMSAVE
+		free( aseq1 );
+		free( aseq2 );
+#else
+		for( i=0; i<icyc; i++ ) strcpy( mseq1[i], aseq1[i] );
+		for( i=0; i<jcyc; i++ ) strcpy( mseq2[i], aseq2[i] );
+
+		FreeCharMtx( aseq1 );
+		FreeCharMtx( aseq2 );
+#endif
+
+//		fprintf( stderr, "value = %f\n", value );
+
+		return( value );
+	}
+//	fprintf( stderr, "Trying to divide the mtx\n" );
+
+	ll1 = ( (int)(lgth1) ) + 100;
+	ll2 = ( (int)(lgth2) ) + 100;
+
+//	fprintf( stderr, "ll1,ll2=%d,%d\n", ll1, ll2 );
+
+	w1 = AllocateFloatVec( ll2+2 );
+	w2 = AllocateFloatVec( ll2+2 );
+//	match = AllocateFloatVec( ll2+2 );
+	midw = AllocateFloatVec( ll2+2 );
+	midn = AllocateFloatVec( ll2+2 );
+	midm = AllocateFloatVec( ll2+2 );
+	jumpbacki = AllocateIntVec( ll2+2 );
+	jumpbackj = AllocateIntVec( ll2+2 );
+	jumpforwi = AllocateIntVec( ll2+2 );
+	jumpforwj = AllocateIntVec( ll2+2 );
+	jumpdummi = AllocateIntVec( ll2+2 );
+	jumpdummj = AllocateIntVec( ll2+2 );
+
+	initverticalw = AllocateFloatVec( ll1+2 );
+	lastverticalw = AllocateFloatVec( ll1+2 );
+
+	m = AllocateFloatVec( ll2+2 );
+	mp = AllocateIntVec( ll2+2 );
+	gaps = AllocateCharVec( MAX( ll1, ll2 ) + 2 );
+
+	floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, nalphabets ); 
+	intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, nalphabets ); 
+
+#if DEBUG
+	fprintf( stderr, "succeeded\n" );
+#endif
+
+#if STOREWM
+	WMMTX = AllocateFloatMtx( ll1, ll2 );
+	WMMTX2 = AllocateFloatMtx( ll1, ll2 );
+#endif
+#if 0
+	shortmtx = AllocateShortMtx( ll1, ll2 );
+
+#if DEBUG
+	fprintf( stderr, "succeeded\n\n" );
+#endif
+
+	ijp = shortmtx;
+#endif
+
+	currentw = w1;
+	previousw = w2;
+
+	match_ribosum( initverticalw, cpmx2+jst, cpmx1+ist, 0, lgth1, floatwork, intwork, 1 );
+
+	match_ribosum( currentw, cpmx1+ist, cpmx2+jst, 0, lgth2, floatwork, intwork, 1 );
+
+	for( i=1; i<lgth1+1; i++ )
+	{
+		initverticalw[i] += ( ogcp1[0] + fgcp1[i-1] );
+	}
+	for( j=1; j<lgth2+1; j++ )
+	{
+		currentw[j] += ( ogcp2[0] + fgcp2[j-1] );
+	}
+
+#if STOREWM
+	WMMTX[0][0] = initverticalw[0];
+	for( i=1; i<lgth1+1; i++ )
+	{
+		WMMTX[i][0] = initverticalw[i];
+	}
+	for( j=1; j<lgth2+1; j++ )
+	{
+		WMMTX[0][j] = currentw[j];
+	}
+#endif
+
+
+	for( j=1; j<lgth2+1; ++j ) 
+	{
+		m[j] = currentw[j-1] + ogcp1[1];
+//		m[j] = currentw[j-1];
+		mp[j] = 0;
+	}
+
+	lastverticalw[0] = currentw[lgth2-1];
+
+	imid = lgth1 * 0.5;
+
+	jumpi = 0; // atode kawaru.
+	lasti = lgth1+1;
+#if STOREWM
+	for( i=1; i<lasti; i++ )
+#else
+	for( i=1; i<=imid; i++ )
+#endif
+	{
+		wtmp = previousw; 
+		previousw = currentw;
+		currentw = wtmp;
+
+		previousw[0] = initverticalw[i-1];
+
+		match_ribosum( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 );
+		currentw[0] = initverticalw[i];
+
+		m[0] = ogcp1[i];
+#if STOREM
+		WMMTX2[i][0] = m[0];
+#endif
+		if( i == imid ) midm[0] = m[0];
+
+		mi = previousw[0] + ogcp2[1]; 
+//		mi = previousw[0];
+		mpi = 0;
+
+
+//		ijppt = ijp[i] + 1;
+		mjpt = m + 1;
+		prept = previousw;
+		curpt = currentw + 1;
+		mpjpt = mp + 1;
+
+
+		lastj = lgth2+1;
+		for( j=1; j<lastj; j++ )
+		{
+
+			wm = *prept;
+
+#if 0
+			fprintf( stderr, "%5.0f->", wm );
+#endif
+			g = mi + fgcp2[j-1];
+//			g = mi + fpenalty;
+#if 0
+			fprintf( stderr, "%5.0f?", g );
+#endif
+			if( g > wm )
+			{
+				wm = g;
+//				*ijppt = -( j - mpi );
+			}
+			g = *prept + ogcp2[j];
+//			g = *prept;
+			if( g >= mi )
+			{
+				mi = g;
+				mpi = j-1;
+			}
+#if USE_PENALTY_EX
+			mi += fpenalty_ex;
+#endif
+
+			g = *mjpt + fgcp1[i-1];
+//			g = *mjpt + fpenalty;
+#if 0 
+			fprintf( stderr, "%5.0f?", g );
+#endif
+			if( g > wm )
+			{
+				wm = g;
+//				*ijppt = +( i - *mpjpt );
+			}
+
+
+			g = *prept + ogcp1[i];
+//			g = *prept;
+			if( g >= *mjpt )
+			{
+				*mjpt = g;
+				*mpjpt = i-1;
+			}
+#if USE_PENALTY_EX
+			m[j] += fpenalty_ex;
+#endif
+#if LOCAL
+            if( wm < localthr )
+            {       
+//				fprintf( stderr, "stop i=%d, j=%d, curpt=%f\n", i, j, *curpt );
+				wm = 0;
+            }       
+#endif
+
+#if 0
+			fprintf( stderr, "%5.0f ", wm );
+#endif
+			*curpt += wm;
+
+
+#if STOREWM
+			WMMTX[i][j] = *curpt;
+			WMMTX2[i][j] = *mjpt;
+#endif
+
+			if( i == imid ) //muda
+			{	
+				jumpbackj[j] = *mpjpt; // muda atode matomeru
+				jumpbacki[j] = mpi; // muda atode matomeru
+//				fprintf( stderr, "jumpbackj[%d] in forward dp is %d\n", j, *mpjpt );
+//				fprintf( stderr, "jumpbacki[%d] in forward dp is %d\n", j, mpi );
+				midw[j] = *curpt;
+				midm[j] = *mjpt;
+				midn[j] = mi;
+			}
+
+//			fprintf( stderr, "m[%d] = %f\n", j, m[j] );
+			mjpt++;
+			prept++;
+			mpjpt++;
+			curpt++;
+
+		}
+		lastverticalw[i] = currentw[lgth2-1];
+
+#if STOREWM
+		WMMTX2[i][lgth2] = m[lgth2-1];
+#endif
+
+#if 0  // ue
+		if( i == imid )
+		{
+			for( j=0; j<lgth2; j++ ) midw[j] = currentw[j];
+			for( j=0; j<lgth2; j++ ) midm[j] = m[j];
+		}
+#endif
+	}
+//	for( j=0; j<lgth2; j++ ) midw[j] = WMMTX[imid][j];
+//	for( j=0; j<lgth2; j++ ) midm[j] = WMMTX2[imid][j];
+
+#if 0
+    for( i=0; i<lgth1; i++ )
+    {
+        for( j=0; j<lgth2; j++ )
+        {
+            fprintf( stderr, "% 10.2f ", WMMTX[i][j] );
+        }
+        fprintf( stderr, "\n" );
+    }
+	fprintf( stderr, "\n" );
+	fprintf( stderr, "WMMTX2 = \n" );
+    for( i=0; i<lgth1; i++ )
+    {
+        for( j=0; j<lgth2; j++ )
+        {
+            fprintf( stderr, "% 10.2f ", WMMTX2[i][j] );
+        }
+        fprintf( stderr, "\n" );
+    }
+	fprintf( stderr, "\n" );
+#endif
+
+// gyakudp
+
+	match_ribosum( initverticalw, cpmx2+jst, cpmx1+ist, lgth2-1, lgth1, floatwork, intwork, 1 );
+	match_ribosum( currentw, cpmx1+ist, cpmx2+jst, lgth1-1, lgth2, floatwork, intwork, 1 );
+
+	for( i=0; i<lgth1-1; i++ )
+	{
+		initverticalw[i] += ( fgcp1[lgth1-1] + ogcp1[i+1] );
+//		initverticalw[i] += fpenalty;
+	}
+	for( j=0; j<lgth2-1; j++ )
+	{
+		currentw[j] += ( fgcp2[lgth2-1] + ogcp2[j+1] );
+//		currentw[j] += fpenalty;
+	}
+
+#if STOREWM
+	for( i=0; i<lgth1-1; i++ )
+	{
+		WMMTX[i][lgth2-1] += ( fgcp1[lgth1-1] + ogcp1[i+1] );
+//		fprintf( stderr, "fgcp1[lgth1-1] + ogcp1[i+1] = %f\n", fgcp1[lgth1-1] + ogcp1[i+1] );
+	}
+	for( j=0; j<lgth2-1; j++ )
+	{
+		WMMTX[lgth1-1][j] += ( fgcp2[lgth2-1] + ogcp2[j+1] );
+//		fprintf( stderr, "fgcp2[lgth2-1] + ogcp2[j+1] = %f\n", fgcp2[lgth2-1] + ogcp2[j+1] );
+	}
+#endif
+
+
+
+
+
+
+	for( j=lgth2-1; j>0; --j )
+	{
+		m[j-1] = currentw[j] + fgcp2[lgth2-2];
+//		m[j-1] = currentw[j];
+		mp[j] = lgth1-1;
+	}
+
+//	for( j=0; j<lgth2; j++ ) m[j] = 0.0;
+	// m[lgth2-1] ha irunoka?
+
+
+//	for( i=lgth1-2; i>=imid; i-- )
+	firstm = -9999999.9;
+	firstmp = lgth1-1;
+	for( i=lgth1-2; i>-1; i-- )
+	{
+		wtmp = previousw;
+		previousw = currentw;
+		currentw = wtmp;
+		previousw[lgth2-1] = initverticalw[i+1];
+//		match_calc( currentw, seq1, seq2, i, lgth2 );
+		match_ribosum( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 );
+
+		currentw[lgth2-1] = initverticalw[i];
+
+//		m[lgth2] = fgcp1[i];
+//		WMMTX2[i][lgth2] += m[lgth2];
+//		fprintf( stderr, "m[] = %f\n", m[lgth2] );
+
+		mi = previousw[lgth2-1] + fgcp2[lgth2-2];
+//		mi = previousw[lgth2-1];
+		mpi = lgth2 - 1;
+
+		mjpt = m + lgth2 - 2;
+		prept = previousw + lgth2 - 1;
+		curpt = currentw + lgth2 - 2;
+		mpjpt = mp + lgth2 - 2;
+
+
+		for( j=lgth2-2; j>-1; j-- )
+		{
+			wm = *prept;
+			ijpi = i+1;
+			ijpj = j+1;
+
+			g = mi + ogcp2[j+1];
+//			g = mi + fpenalty;
+			if( g > wm )
+			{
+				wm = g;
+				ijpj = mpi;
+				ijpi = i+1;
+			}
+
+			g = *prept + fgcp2[j];
+//			g = *prept;
+			if( g >= mi )
+			{
+//				fprintf( stderr, "i,j=%d,%d - renewed! mpi = %d\n", i, j, j+1 );
+				mi = g;
+				mpi = j + 1;
+			}
+
+#if USE_PENALTY_EX
+			mi += fpenalty_ex;
+#endif
+
+//			fprintf( stderr, "i,j=%d,%d *mpjpt = %d\n", i, j, *mpjpt );
+			g = *mjpt + ogcp1[i+1];
+//			g = *mjpt + fpenalty;
+			if( g > wm )
+			{
+				wm = g;
+				ijpi = *mpjpt;
+				ijpj = j+1;
+			}
+
+//			if( i == imid )fprintf( stderr, "i,j=%d,%d \n", i, j );
+			g = *prept + fgcp1[i];
+//			g = *prept;
+			if( g >= *mjpt )
+			{
+				*mjpt = g;
+				*mpjpt = i + 1;
+			}
+
+#if USE_PENALTY_EX
+			m[j] += fpenalty_ex;
+#endif
+
+			if( i == jumpi || i == imid - 1 )
+			{
+				jumpforwi[j] = ijpi; //muda
+				jumpforwj[j] = ijpj; //muda
+//				fprintf( stderr, "jumpfori[%d] = %d\n", j, ijpi );
+//				fprintf( stderr, "jumpforj[%d] = %d\n", j, ijpj );
+			}
+			if( i == imid ) // muda
+			{
+				midw[j] += wm;
+//				midm[j+1] += *mjpt + fpenalty; //??????
+				midm[j+1] += *mjpt; //??????
+			}
+			if( i == imid - 1 )
+			{
+//				midn[j] += mi + fpenalty;  //????
+				midn[j] += mi;  //????
+			}
+#if LOCAL
+            if( wm < localthr )
+            {       
+//				fprintf( stderr, "stop i=%d, j=%d, curpt=%f\n", i, j, *curpt );
+				wm = 0;
+            }       
+#endif
+
+#if STOREWM
+			WMMTX[i][j] += wm;
+//			WMMTX2[i][j+1] += *mjpt + fpenalty;
+			WMMTX2[i][j] += *curpt;
+#endif
+			*curpt += wm;
+
+			mjpt--;
+			prept--;
+			mpjpt--;
+			curpt--;
+		}
+//		fprintf( stderr, "adding *mjpt (=%f) to WMMTX2[%d][%d]\n", *mjpt, i, j+1 );
+		g = *prept + fgcp1[i];
+		if( firstm < g ) 
+		{
+			firstm = g;
+			firstmp = i + 1;
+		}
+#if STOREWM
+//		WMMTX2[i][j+1] += firstm;
+#endif
+		if( i == imid ) midm[j+1] += firstm;
+
+		if( i == imid - 1 )	
+		{
+			maxwm = midw[1];
+			jmid = 0;
+//			if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
+			for( j=2; j<lgth2-1; j++ )
+			{
+				wm = midw[j];
+				if( wm > maxwm )
+				{
+					jmid = j;
+					maxwm = wm;
+				}
+//				if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
+			}
+			for( j=0; j<lgth2+1; j++ )
+			{
+				wm = midm[j];
+				if( wm > maxwm )
+				{
+					jmid = j;
+					maxwm = wm;
+				}
+//				if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
+			}
+
+//			if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
+
+
+//			fprintf( stderr, "### imid=%d, jmid=%d\n", imid, jmid );
+			wm = midw[jmid];
+			jumpi = imid-1;
+			jumpj = jmid-1;
+			if( jmid > 0 && midn[jmid-1] > wm ) //060413
+			{
+				jumpi = imid-1;
+				jumpj = jumpbacki[jmid];
+				wm = midn[jmid-1];
+//				fprintf( stderr, "rejump (n)\n" );
+			}
+			if( midm[jmid] > wm )
+			{
+				jumpi = jumpbackj[jmid];
+				jumpj = jmid-1;
+				wm = midm[jmid];
+//				fprintf( stderr, "rejump (m) jumpi=%d\n", jumpi );
+			}
+
+
+//			fprintf( stderr, "--> imid=%d, jmid=%d\n", imid, jmid );
+//			fprintf( stderr, "--> jumpi=%d, jumpj=%d\n", jumpi, jumpj );
+#if 0
+			fprintf( stderr, "imid = %d\n", imid );
+			fprintf( stderr, "midn = \n" );
+			for( j=0; j<lgth2; j++ )
+			{
+				fprintf( stderr, "% 7.1f ", midn[j] );
+			}
+			fprintf( stderr, "\n" );
+			fprintf( stderr, "midw = \n" );
+			for( j=0; j<lgth2; j++ )
+			{
+				fprintf( stderr, "% 7.1f ", midw[j] );
+			}
+			fprintf( stderr, "\n" );
+			fprintf( stderr, "midm = \n" );
+			for( j=0; j<lgth2; j++ )
+			{
+				fprintf( stderr, "% 7.1f ", midm[j] );
+			}
+			fprintf( stderr, "\n" );
+#endif
+//			fprintf( stderr, "maxwm = %f\n", maxwm );
+		}
+		if( i == jumpi ) //saki?
+		{
+//			fprintf( stderr, "imid, jumpi = %d,%d\n", imid, jumpi );
+//			fprintf( stderr, "jmid, jumpj = %d,%d\n", jmid, jumpj );
+			if( jmid == 0 )
+			{
+//				fprintf( stderr, "CHUI2!\n" );
+				jumpj = 0; jmid = 1;
+				jumpi = firstmp - 1;
+				imid = firstmp;
+			}
+
+#if 0
+			else if( jmid == lgth2 ) 
+			{
+				fprintf( stderr, "CHUI1!\n" );
+				jumpi=0; jumpj=0;
+				imid=jumpforwi[0]; jmid=lgth2-1;
+			}
+#else // 060414
+			else if( jmid >= lgth2 ) 
+			{
+//				fprintf( stderr, "CHUI1!\n" );
+				jumpi=imid-1; jmid=lgth2;
+				jumpj = lgth2-1;
+			}
+#endif
+			else
+			{
+				imid = jumpforwi[jumpj];
+				jmid = jumpforwj[jumpj];
+			}
+#if 0
+			fprintf( stderr, "jumpi -> %d\n", jumpi );
+			fprintf( stderr, "jumpj -> %d\n", jumpj );
+			fprintf( stderr, "imid -> %d\n", imid );
+			fprintf( stderr, "jmid -> %d\n", jmid );
+#endif
+
+#if STOREWM
+//			break;
+#else
+			break;
+#endif
+		}
+	}
+#if 0
+		jumpi=0; jumpj=0;
+		imid=lgth1-1; jmid=lgth2-1;
+	}
+#endif
+
+//	fprintf( stderr, "imid = %d, but jumpi = %d\n", imid, jumpi );
+//	fprintf( stderr, "jmid = %d, but jumpj = %d\n", jmid, jumpj );
+
+//	for( j=0; j<lgth2; j++ ) midw[j] += currentw[j];
+//	for( j=0; j<lgth2; j++ ) midm[j] += m[j+1];
+//	for( j=0; j<lgth2; j++ ) midw[j] += WMMTX[imid][j];
+//	for( j=0; j<lgth2; j++ ) midw[j] += WMMTX[imid][j];
+
+
+
+	for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ )
+		map[i][j] = WMMTX[i][j] / maxwm;
+//		map[i][j] = WMMTX2[i][j] / maxwm;
+
+#if STOREWM
+
+#if 0
+	for( i=0; i<lgth1; i++ )
+	{
+		float maxpairscore = -9999.9;
+		float tmpscore;
+
+		for( j=0; j<lgth2; j++ )
+		{
+			if( maxpairscore < (tmpscore=WMMTX[i][j]) )
+			{
+				map12[i].pos = j;
+				map12[i].score = tmpscore;
+				maxpairscore = tmpscore;
+			}
+		}
+
+		for( k=0; k<lgth1; k++ )
+		{
+			if( i == k ) continue;
+			if( map12[i].score <= WMMTX[k][map12[i].pos] )
+				break;
+		}
+		if( k != lgth1 )
+		{
+			map12[i].pos = -1;
+			map12[i].score = -1.0;
+		}
+		fprintf( stderr, "pair of %d = %d (%f) %c:%c\n", i, map12[i].pos, map12[i].score, seq1[0][i], seq2[0][map12[i].pos] );
+	}
+	for( j=0; j<lgth2; j++ )
+	{
+		float maxpairscore = -9999.9;
+		float tmpscore;
+
+		for( i=0; i<lgth1; i++ )
+		{
+			if( maxpairscore < (tmpscore=WMMTX[i][j]) )
+			{
+				map21[j].pos = i;
+				map21[j].score = tmpscore;
+				maxpairscore = tmpscore;
+			}
+		}
+
+		for( k=0; k<lgth2; k++ )
+		{
+			if( j == k ) continue;
+			if( map21[j].score <= WMMTX[map21[j].pos][k] )
+				break;
+		}
+		if( k != lgth2 )
+		{
+			map21[j].pos = -1;
+			map21[j].score = -1.0;
+		}
+		fprintf( stderr, "pair of %d = %d (%f) %c:%c\n", j, map21[j].pos, map21[j].score, seq2[0][j], seq1[0][map21[j].pos] );
+	}
+
+	for( i=0; i<lgth1; i++ )
+	{
+		if( map12[i].pos != -1 ) if( map21[map12[i].pos].pos != i ) 
+			fprintf( stderr, "ERROR i=%d, but map12[i].pos=%d and map21[map12[i].pos]=%d\n", i, map12[i].pos, map21[map12[i].pos].pos );
+	}
+#endif
+
+#if 0
+	fprintf( stderr, "WMMTX = \n" );
+    for( i=0; i<lgth1; i++ )
+    {
+        fprintf( stderr, "%d ", i );
+        for( j=0; j<lgth2; j++ )
+        {
+            fprintf( stderr, "% 7.2f ", WMMTX[i][j] );
+        }
+        fprintf( stderr, "\n" );
+    }
+//	fprintf( stderr, "WMMTX2 = (p = %f)\n", fpenalty );
+    for( i=0; i<lgth1; i++ )
+    {
+        fprintf( stderr, "%d ", i );
+        for( j=0; j<lgth2+1; j++ )
+        {
+            fprintf( stderr, "% 7.2f ", WMMTX2[i][j] );
+        }
+        fprintf( stderr, "\n" );
+    }
+#endif
+
+#if 0
+    fprintf( stdout, "#WMMTX = \n" );
+    for( i=0; i<lgth1; i++ )
+    {
+//        fprintf( stdout, "%d ", i ); 
+        for( j=0; j<lgth2; j++ )
+        {
+//          if( WMMTX[i][j] > amino_dis['a']['g'] -1 )
+                fprintf( stdout, "%d %d %8.1f", i, j, WMMTX[i][j] );
+			if( WMMTX[i][j] == maxwm )
+                fprintf( stdout, "selected \n" );
+			else
+                fprintf( stdout, "\n" );
+        }
+        fprintf( stdout, "\n" );
+    }
+#endif
+
+#if 0
+
+	fprintf( stderr, "jumpbacki = \n" );
+	for( j=0; j<lgth2; j++ )
+	{
+		fprintf( stderr, "% 7d ", jumpbacki[j] );
+	}
+	fprintf( stderr, "\n" );
+	fprintf( stderr, "jumpbackj = \n" );
+	for( j=0; j<lgth2; j++ )
+	{
+		fprintf( stderr, "% 7d ", jumpbackj[j] );
+	}
+	fprintf( stderr, "\n" );
+	fprintf( stderr, "jumpforwi = \n" );
+	for( j=0; j<lgth2; j++ )
+	{
+		fprintf( stderr, "% 7d ", jumpforwi[j] );
+	}
+	fprintf( stderr, "\n" );
+	fprintf( stderr, "jumpforwj = \n" );
+	for( j=0; j<lgth2; j++ )
+	{
+		fprintf( stderr, "% 7d ", jumpforwj[j] );
+	}
+	fprintf( stderr, "\n" );
+#endif
+
+
+#endif
+
+
+//	Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );
+
+#if 0 // irukamo
+	resultlen = strlen( mseq1[0] );
+	if( alloclen < resultlen || resultlen > N )
+	{
+		fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
+		ErrorExit( "LENGTH OVER!\n" );
+	}
+#endif
+
+
+
+#if 0
+	fprintf( stderr, "jumpi = %d, imid = %d\n", jumpi, imid );
+	fprintf( stderr, "jumpj = %d, jmid = %d\n", jumpj, jmid );
+
+	fprintf( stderr, "imid = %d\n", imid );
+	fprintf( stderr, "jmid = %d\n", jmid );
+#endif
+
+
+	FreeFloatVec( w1 );
+	FreeFloatVec( w2 );
+	FreeFloatVec( initverticalw );
+	FreeFloatVec( lastverticalw );
+	FreeFloatVec( midw );
+	FreeFloatVec( midm );
+	FreeFloatVec( midn );
+
+	FreeIntVec( jumpbacki );
+	FreeIntVec( jumpbackj );
+	FreeIntVec( jumpforwi );
+	FreeIntVec( jumpforwj );
+	FreeIntVec( jumpdummi );
+	FreeIntVec( jumpdummj );
+
+	FreeFloatVec( m );
+	FreeIntVec( mp );
+
+	FreeFloatMtx( floatwork );
+	FreeIntMtx( intwork );
+
+#if STOREWM
+	FreeFloatMtx( WMMTX );
+	FreeFloatMtx( WMMTX2 );
+#endif
+
+	return( value );
+
+}
+static float MSalignmm_rec( int icyc, int jcyc, double *eff1, double *eff2, char **seq1, char **seq2, float **cpmx1, float **cpmx2, int ist, int ien, int jst, int jen, int alloclen, char **mseq1, char **mseq2, int depth, float **gapinfo, float **map )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+	float value = 0.0;
+	register int i, j;
+	char **aseq1, **aseq2;
+	int ll1, ll2;
+	int lasti, lastj, imid, jmid=0;
+	float wm = 0.0;   /* int ?????? */
+	float g;
+	float *currentw, *previousw;
+#if USE_PENALTY_EX
+	float fpenalty_ex = (float)RNApenalty_ex;
+#endif
+//	float fpenalty = (float)penalty;
+	float *wtmp;
+//	short *ijppt;
+	int *mpjpt;
+//	short **ijp;
+	int *mp;
+	int mpi;
+	float *mjpt, *prept, *curpt;
+	float mi;
+	float *m;
+	float *w1, *w2;
+//	float *match;
+	float *initverticalw;    /* kufuu sureba iranai */
+	float *lastverticalw;    /* kufuu sureba iranai */
+	int **intwork;
+	float **floatwork;
+//	short **shortmtx;
+#if STOREWM
+	float **WMMTX;
+	float **WMMTX2;
+#endif
+	float *midw;
+	float *midm;
+	float *midn;
+	int lgth1, lgth2;
+	float maxwm = 0.0;
+	int *jumpforwi;
+	int *jumpforwj;
+	int *jumpbacki;
+	int *jumpbackj;
+	int *jumpdummi; //muda
+	int *jumpdummj; //muda
+	int jumpi, jumpj = 0;
+	char *gaps;
+	int ijpi, ijpj;
+	float *ogcp1;
+	float *fgcp1;
+	float *ogcp2;
+	float *fgcp2;
+	float firstm;
+	int firstmp;
+#if 0
+	static char ttt1[50000];
+	static char ttt2[50000];
+#endif
+
+	localthr = -offset + 500; // 0?
+
+	ogcp1 = gapinfo[0] + ist;
+	fgcp1 = gapinfo[1] + ist;
+	ogcp2 = gapinfo[2] + jst;
+	fgcp2 = gapinfo[3] + jst;
+
+	depth++;
+	reccycle++;
+
+	lgth1 = ien-ist+1;
+	lgth2 = jen-jst+1;
+
+//	if( lgth1 < 5 )
+//		fprintf( stderr, "\nWARNING: lgth1 = %d\n", lgth1 );
+//	if( lgth2 < 5 )
+//		fprintf( stderr, "\nWARNING: lgth2 = %d\n", lgth2 );
+//
+
+#if 0
+	fprintf( stderr, "==== MSalign (depth=%d, reccycle=%d), ist=%d, ien=%d, jst=%d, jen=%d\n", depth, reccycle, ist, ien, jst, jen );
+	strncpy( ttt1, seq1[0]+ist, lgth1 );
+	strncpy( ttt2, seq2[0]+jst, lgth2 );
+	ttt1[lgth1] = 0;
+	ttt2[lgth2] = 0;
+	fprintf( stderr, "seq1 = %s\n", ttt1 );
+	fprintf( stderr, "seq2 = %s\n", ttt2 );
+#endif
+	if( lgth2 <= 0 ) // lgth1 <= 0 ha?
+	{
+//		fprintf( stderr, "\n\n==== jimei\n\n" );
+//		exit( 1 );
+		for( i=0; i<icyc; i++ ) 
+		{
+			strncpy( mseq1[i], seq1[i]+ist, lgth1 );
+			mseq1[i][lgth1] = 0;
+		}
+		for( i=0; i<jcyc; i++ ) 
+		{
+			mseq2[i][0] = 0;
+			for( j=0; j<lgth1; j++ )
+				strcat( mseq2[i], "-" );
+		}
+
+//		fprintf( stderr, "==== mseq1[0] (%d) = %s\n", depth, mseq1[0] );
+//		fprintf( stderr, "==== mseq2[0] (%d) = %s\n", depth, mseq2[0] );
+
+		return( 0.0 );
+	}
+
+#if MEMSAVE
+	aseq1 = AllocateCharMtx( icyc, 0 );
+	aseq2 = AllocateCharMtx( jcyc, 0 );
+	for( i=0; i<icyc; i++ ) aseq1[i] = mseq1[i];
+	for( i=0; i<jcyc; i++ ) aseq2[i] = mseq2[i];
+#else
+	aseq1 = AllocateCharMtx( icyc, lgth1+lgth2+100 );
+	aseq2 = AllocateCharMtx( jcyc, lgth1+lgth2+100 );
+#endif
+
+//  if( lgth1 < DPTANNI && lgth2 < DPTANNI ) // & dato lgth ==1 no kanousei ga arunode yokunai 
+//    if( lgth1 < DPTANNI ) // kore mo lgth2 ga mijikasugiru kanousei ari
+    if( lgth1 < DPTANNI || lgth2 < DPTANNI ) // zettai ni anzen ka?
+	{
+//		fprintf( stderr, "==== Going to _tanni\n" );
+
+//		value = MSalignmm_tanni( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist, ien, jst, jen, alloclen, aseq1, aseq2, gapinfo );	
+
+
+#if MEMSAVE
+		free( aseq1 );
+		free( aseq2 );
+#else
+		for( i=0; i<icyc; i++ ) strcpy( mseq1[i], aseq1[i] );
+		for( i=0; i<jcyc; i++ ) strcpy( mseq2[i], aseq2[i] );
+
+		FreeCharMtx( aseq1 );
+		FreeCharMtx( aseq2 );
+#endif
+
+//		fprintf( stderr, "value = %f\n", value );
+
+		return( value );
+	}
+//	fprintf( stderr, "Trying to divide the mtx\n" );
+
+	ll1 = ( (int)(lgth1) ) + 100;
+	ll2 = ( (int)(lgth2) ) + 100;
+
+//	fprintf( stderr, "ll1,ll2=%d,%d\n", ll1, ll2 );
+
+	w1 = AllocateFloatVec( ll2+2 );
+	w2 = AllocateFloatVec( ll2+2 );
+//	match = AllocateFloatVec( ll2+2 );
+	midw = AllocateFloatVec( ll2+2 );
+	midn = AllocateFloatVec( ll2+2 );
+	midm = AllocateFloatVec( ll2+2 );
+	jumpbacki = AllocateIntVec( ll2+2 );
+	jumpbackj = AllocateIntVec( ll2+2 );
+	jumpforwi = AllocateIntVec( ll2+2 );
+	jumpforwj = AllocateIntVec( ll2+2 );
+	jumpdummi = AllocateIntVec( ll2+2 );
+	jumpdummj = AllocateIntVec( ll2+2 );
+
+	initverticalw = AllocateFloatVec( ll1+2 );
+	lastverticalw = AllocateFloatVec( ll1+2 );
+
+	m = AllocateFloatVec( ll2+2 );
+	mp = AllocateIntVec( ll2+2 );
+	gaps = AllocateCharVec( MAX( ll1, ll2 ) + 2 );
+
+	floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, nalphabets ); 
+	intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, nalphabets ); 
+
+#if DEBUG
+	fprintf( stderr, "succeeded\n" );
+#endif
+
+#if STOREWM
+	WMMTX = AllocateFloatMtx( ll1, ll2 );
+	WMMTX2 = AllocateFloatMtx( ll1, ll2 );
+#endif
+#if 0
+	shortmtx = AllocateShortMtx( ll1, ll2 );
+
+#if DEBUG
+	fprintf( stderr, "succeeded\n\n" );
+#endif
+
+	ijp = shortmtx;
+#endif
+
+	currentw = w1;
+	previousw = w2;
+
+	match_calc( initverticalw, cpmx2+jst, cpmx1+ist, 0, lgth1, floatwork, intwork, 1 );
+
+	match_calc( currentw, cpmx1+ist, cpmx2+jst, 0, lgth2, floatwork, intwork, 1 );
+
+	for( i=1; i<lgth1+1; i++ )
+	{
+		initverticalw[i] += ( ogcp1[0] + fgcp1[i-1] );
+	}
+	for( j=1; j<lgth2+1; j++ )
+	{
+		currentw[j] += ( ogcp2[0] + fgcp2[j-1] );
+	}
+
+#if STOREWM
+	WMMTX[0][0] = initverticalw[0];
+	for( i=1; i<lgth1+1; i++ )
+	{
+		WMMTX[i][0] = initverticalw[i];
+	}
+	for( j=1; j<lgth2+1; j++ )
+	{
+		WMMTX[0][j] = currentw[j];
+	}
+#endif
+
+
+	for( j=1; j<lgth2+1; ++j ) 
+	{
+		m[j] = currentw[j-1] + ogcp1[1];
+//		m[j] = currentw[j-1];
+		mp[j] = 0;
+	}
+
+	lastverticalw[0] = currentw[lgth2-1];
+
+	imid = lgth1 * 0.5;
+
+	jumpi = 0; // atode kawaru.
+	lasti = lgth1+1;
+#if STOREWM
+	for( i=1; i<lasti; i++ )
+#else
+	for( i=1; i<=imid; i++ )
+#endif
+	{
+		wtmp = previousw; 
+		previousw = currentw;
+		currentw = wtmp;
+
+		previousw[0] = initverticalw[i-1];
+
+		match_calc( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 );
+		currentw[0] = initverticalw[i];
+
+		m[0] = ogcp1[i];
+#if STOREM
+		WMMTX2[i][0] = m[0];
+#endif
+		if( i == imid ) midm[0] = m[0];
+
+		mi = previousw[0] + ogcp2[1]; 
+//		mi = previousw[0];
+		mpi = 0;
+
+
+//		ijppt = ijp[i] + 1;
+		mjpt = m + 1;
+		prept = previousw;
+		curpt = currentw + 1;
+		mpjpt = mp + 1;
+
+
+		lastj = lgth2+1;
+		for( j=1; j<lastj; j++ )
+		{
+
+			wm = *prept;
+
+#if 0
+			fprintf( stderr, "%5.0f->", wm );
+#endif
+			g = mi + fgcp2[j-1];
+//			g = mi + fpenalty;
+#if 0
+			fprintf( stderr, "%5.0f?", g );
+#endif
+			if( g > wm )
+			{
+				wm = g;
+//				*ijppt = -( j - mpi );
+			}
+			g = *prept + ogcp2[j];
+//			g = *prept;
+			if( g >= mi )
+			{
+				mi = g;
+				mpi = j-1;
+			}
+#if USE_PENALTY_EX
+			mi += fpenalty_ex;
+#endif
+
+			g = *mjpt + fgcp1[i-1];
+//			g = *mjpt + fpenalty;
+#if 0 
+			fprintf( stderr, "%5.0f?", g );
+#endif
+			if( g > wm )
+			{
+				wm = g;
+//				*ijppt = +( i - *mpjpt );
+			}
+
+
+			g = *prept + ogcp1[i];
+//			g = *prept;
+			if( g >= *mjpt )
+			{
+				*mjpt = g;
+				*mpjpt = i-1;
+			}
+#if USE_PENALTY_EX
+			m[j] += fpenalty_ex;
+#endif
+#if LOCAL
+            if( wm < localthr )
+            {       
+//				fprintf( stderr, "stop i=%d, j=%d, curpt=%f\n", i, j, *curpt );
+				wm = 0;
+            }       
+#endif
+
+#if 0
+			fprintf( stderr, "%5.0f ", wm );
+#endif
+			*curpt += wm;
+
+
+#if STOREWM
+			WMMTX[i][j] = *curpt;
+			WMMTX2[i][j] = *mjpt;
+#endif
+
+			if( i == imid ) //muda
+			{	
+				jumpbackj[j] = *mpjpt; // muda atode matomeru
+				jumpbacki[j] = mpi; // muda atode matomeru
+//				fprintf( stderr, "jumpbackj[%d] in forward dp is %d\n", j, *mpjpt );
+//				fprintf( stderr, "jumpbacki[%d] in forward dp is %d\n", j, mpi );
+				midw[j] = *curpt;
+				midm[j] = *mjpt;
+				midn[j] = mi;
+			}
+
+//			fprintf( stderr, "m[%d] = %f\n", j, m[j] );
+			mjpt++;
+			prept++;
+			mpjpt++;
+			curpt++;
+
+		}
+		lastverticalw[i] = currentw[lgth2-1];
+
+#if STOREWM
+		WMMTX2[i][lgth2] = m[lgth2-1];
+#endif
+
+#if 0  // ue
+		if( i == imid )
+		{
+			for( j=0; j<lgth2; j++ ) midw[j] = currentw[j];
+			for( j=0; j<lgth2; j++ ) midm[j] = m[j];
+		}
+#endif
+	}
+//	for( j=0; j<lgth2; j++ ) midw[j] = WMMTX[imid][j];
+//	for( j=0; j<lgth2; j++ ) midm[j] = WMMTX2[imid][j];
+
+#if 0
+    for( i=0; i<lgth1; i++ )
+    {
+        for( j=0; j<lgth2; j++ )
+        {
+            fprintf( stderr, "% 10.2f ", WMMTX[i][j] );
+        }
+        fprintf( stderr, "\n" );
+    }
+	fprintf( stderr, "\n" );
+	fprintf( stderr, "WMMTX2 = \n" );
+    for( i=0; i<lgth1; i++ )
+    {
+        for( j=0; j<lgth2; j++ )
+        {
+            fprintf( stderr, "% 10.2f ", WMMTX2[i][j] );
+        }
+        fprintf( stderr, "\n" );
+    }
+	fprintf( stderr, "\n" );
+#endif
+
+// gyakudp
+
+	match_calc( initverticalw, cpmx2+jst, cpmx1+ist, lgth2-1, lgth1, floatwork, intwork, 1 );
+	match_calc( currentw, cpmx1+ist, cpmx2+jst, lgth1-1, lgth2, floatwork, intwork, 1 );
+
+	for( i=0; i<lgth1-1; i++ )
+	{
+		initverticalw[i] += ( fgcp1[lgth1-1] + ogcp1[i+1] );
+//		initverticalw[i] += fpenalty;
+	}
+	for( j=0; j<lgth2-1; j++ )
+	{
+		currentw[j] += ( fgcp2[lgth2-1] + ogcp2[j+1] );
+//		currentw[j] += fpenalty;
+	}
+
+#if STOREWM
+	for( i=0; i<lgth1-1; i++ )
+	{
+		WMMTX[i][lgth2-1] += ( fgcp1[lgth1-1] + ogcp1[i+1] );
+//		fprintf( stderr, "fgcp1[lgth1-1] + ogcp1[i+1] = %f\n", fgcp1[lgth1-1] + ogcp1[i+1] );
+	}
+	for( j=0; j<lgth2-1; j++ )
+	{
+		WMMTX[lgth1-1][j] += ( fgcp2[lgth2-1] + ogcp2[j+1] );
+//		fprintf( stderr, "fgcp2[lgth2-1] + ogcp2[j+1] = %f\n", fgcp2[lgth2-1] + ogcp2[j+1] );
+	}
+#endif
+
+
+
+
+
+
+	for( j=lgth2-1; j>0; --j )
+	{
+		m[j-1] = currentw[j] + fgcp2[lgth2-2];
+//		m[j-1] = currentw[j];
+		mp[j] = lgth1-1;
+	}
+
+//	for( j=0; j<lgth2; j++ ) m[j] = 0.0;
+	// m[lgth2-1] ha irunoka?
+
+
+//	for( i=lgth1-2; i>=imid; i-- )
+	firstm = -9999999.9;
+	firstmp = lgth1-1;
+	for( i=lgth1-2; i>-1; i-- )
+	{
+		wtmp = previousw;
+		previousw = currentw;
+		currentw = wtmp;
+		previousw[lgth2-1] = initverticalw[i+1];
+//		match_calc( currentw, seq1, seq2, i, lgth2 );
+		match_calc( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 );
+
+		currentw[lgth2-1] = initverticalw[i];
+
+//		m[lgth2] = fgcp1[i];
+//		WMMTX2[i][lgth2] += m[lgth2];
+//		fprintf( stderr, "m[] = %f\n", m[lgth2] );
+
+		mi = previousw[lgth2-1] + fgcp2[lgth2-2];
+//		mi = previousw[lgth2-1];
+		mpi = lgth2 - 1;
+
+		mjpt = m + lgth2 - 2;
+		prept = previousw + lgth2 - 1;
+		curpt = currentw + lgth2 - 2;
+		mpjpt = mp + lgth2 - 2;
+
+
+		for( j=lgth2-2; j>-1; j-- )
+		{
+			wm = *prept;
+			ijpi = i+1;
+			ijpj = j+1;
+
+			g = mi + ogcp2[j+1];
+//			g = mi + fpenalty;
+			if( g > wm )
+			{
+				wm = g;
+				ijpj = mpi;
+				ijpi = i+1;
+			}
+
+			g = *prept + fgcp2[j];
+//			g = *prept;
+			if( g >= mi )
+			{
+//				fprintf( stderr, "i,j=%d,%d - renewed! mpi = %d\n", i, j, j+1 );
+				mi = g;
+				mpi = j + 1;
+			}
+
+#if USE_PENALTY_EX
+			mi += fpenalty_ex;
+#endif
+
+//			fprintf( stderr, "i,j=%d,%d *mpjpt = %d\n", i, j, *mpjpt );
+			g = *mjpt + ogcp1[i+1];
+//			g = *mjpt + fpenalty;
+			if( g > wm )
+			{
+				wm = g;
+				ijpi = *mpjpt;
+				ijpj = j+1;
+			}
+
+//			if( i == imid )fprintf( stderr, "i,j=%d,%d \n", i, j );
+			g = *prept + fgcp1[i];
+//			g = *prept;
+			if( g >= *mjpt )
+			{
+				*mjpt = g;
+				*mpjpt = i + 1;
+			}
+
+#if USE_PENALTY_EX
+			m[j] += fpenalty_ex;
+#endif
+
+			if( i == jumpi || i == imid - 1 )
+			{
+				jumpforwi[j] = ijpi; //muda
+				jumpforwj[j] = ijpj; //muda
+//				fprintf( stderr, "jumpfori[%d] = %d\n", j, ijpi );
+//				fprintf( stderr, "jumpforj[%d] = %d\n", j, ijpj );
+			}
+			if( i == imid ) // muda
+			{
+				midw[j] += wm;
+//				midm[j+1] += *mjpt + fpenalty; //??????
+				midm[j+1] += *mjpt; //??????
+			}
+			if( i == imid - 1 )
+			{
+//				midn[j] += mi + fpenalty;  //????
+				midn[j] += mi;  //????
+			}
+#if LOCAL
+            if( wm < localthr )
+            {       
+//				fprintf( stderr, "stop i=%d, j=%d, curpt=%f\n", i, j, *curpt );
+				wm = 0;
+            }       
+#endif
+
+#if STOREWM
+			WMMTX[i][j] += wm;
+//			WMMTX2[i][j+1] += *mjpt + fpenalty;
+			WMMTX2[i][j] += *curpt;
+#endif
+			*curpt += wm;
+
+			mjpt--;
+			prept--;
+			mpjpt--;
+			curpt--;
+		}
+//		fprintf( stderr, "adding *mjpt (=%f) to WMMTX2[%d][%d]\n", *mjpt, i, j+1 );
+		g = *prept + fgcp1[i];
+		if( firstm < g ) 
+		{
+			firstm = g;
+			firstmp = i + 1;
+		}
+#if STOREWM
+//		WMMTX2[i][j+1] += firstm;
+#endif
+		if( i == imid ) midm[j+1] += firstm;
+
+		if( i == imid - 1 )	
+		{
+			maxwm = midw[1];
+			jmid = 0;
+//			if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
+			for( j=2; j<lgth2-1; j++ )
+			{
+				wm = midw[j];
+				if( wm > maxwm )
+				{
+					jmid = j;
+					maxwm = wm;
+				}
+//				if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
+			}
+			for( j=0; j<lgth2+1; j++ )
+			{
+				wm = midm[j];
+				if( wm > maxwm )
+				{
+					jmid = j;
+					maxwm = wm;
+				}
+//				if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
+			}
+
+//			if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
+
+
+//			fprintf( stderr, "### imid=%d, jmid=%d\n", imid, jmid );
+			wm = midw[jmid];
+			jumpi = imid-1;
+			jumpj = jmid-1;
+			if( jmid > 0 && midn[jmid-1] > wm ) //060413
+			{
+				jumpi = imid-1;
+				jumpj = jumpbacki[jmid];
+				wm = midn[jmid-1];
+//				fprintf( stderr, "rejump (n)\n" );
+			}
+			if( midm[jmid] > wm )
+			{
+				jumpi = jumpbackj[jmid];
+				jumpj = jmid-1;
+				wm = midm[jmid];
+//				fprintf( stderr, "rejump (m) jumpi=%d\n", jumpi );
+			}
+
+
+//			fprintf( stderr, "--> imid=%d, jmid=%d\n", imid, jmid );
+//			fprintf( stderr, "--> jumpi=%d, jumpj=%d\n", jumpi, jumpj );
+#if 0
+			fprintf( stderr, "imid = %d\n", imid );
+			fprintf( stderr, "midn = \n" );
+			for( j=0; j<lgth2; j++ )
+			{
+				fprintf( stderr, "% 7.1f ", midn[j] );
+			}
+			fprintf( stderr, "\n" );
+			fprintf( stderr, "midw = \n" );
+			for( j=0; j<lgth2; j++ )
+			{
+				fprintf( stderr, "% 7.1f ", midw[j] );
+			}
+			fprintf( stderr, "\n" );
+			fprintf( stderr, "midm = \n" );
+			for( j=0; j<lgth2; j++ )
+			{
+				fprintf( stderr, "% 7.1f ", midm[j] );
+			}
+			fprintf( stderr, "\n" );
+#endif
+//			fprintf( stderr, "maxwm = %f\n", maxwm );
+		}
+		if( i == jumpi ) //saki?
+		{
+//			fprintf( stderr, "imid, jumpi = %d,%d\n", imid, jumpi );
+//			fprintf( stderr, "jmid, jumpj = %d,%d\n", jmid, jumpj );
+			if( jmid == 0 )
+			{
+//				fprintf( stderr, "CHUI2!\n" );
+				jumpj = 0; jmid = 1;
+				jumpi = firstmp - 1;
+				imid = firstmp;
+			}
+
+#if 0
+			else if( jmid == lgth2 ) 
+			{
+				fprintf( stderr, "CHUI1!\n" );
+				jumpi=0; jumpj=0;
+				imid=jumpforwi[0]; jmid=lgth2-1;
+			}
+#else // 060414
+			else if( jmid >= lgth2 ) 
+			{
+//				fprintf( stderr, "CHUI1!\n" );
+				jumpi=imid-1; jmid=lgth2;
+				jumpj = lgth2-1;
+			}
+#endif
+			else
+			{
+				imid = jumpforwi[jumpj];
+				jmid = jumpforwj[jumpj];
+			}
+#if 0
+			fprintf( stderr, "jumpi -> %d\n", jumpi );
+			fprintf( stderr, "jumpj -> %d\n", jumpj );
+			fprintf( stderr, "imid -> %d\n", imid );
+			fprintf( stderr, "jmid -> %d\n", jmid );
+#endif
+
+#if STOREWM
+//			break;
+#else
+			break;
+#endif
+		}
+	}
+#if 0
+		jumpi=0; jumpj=0;
+		imid=lgth1-1; jmid=lgth2-1;
+	}
+#endif
+
+//	fprintf( stderr, "imid = %d, but jumpi = %d\n", imid, jumpi );
+//	fprintf( stderr, "jmid = %d, but jumpj = %d\n", jmid, jumpj );
+
+//	for( j=0; j<lgth2; j++ ) midw[j] += currentw[j];
+//	for( j=0; j<lgth2; j++ ) midm[j] += m[j+1];
+//	for( j=0; j<lgth2; j++ ) midw[j] += WMMTX[imid][j];
+//	for( j=0; j<lgth2; j++ ) midw[j] += WMMTX[imid][j];
+
+
+
+	for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ )
+		map[i][j] = WMMTX[i][j] / maxwm;
+//		map[i][j] = WMMTX2[i][j] / maxwm;
+
+#if STOREWM
+
+#if 0
+	for( i=0; i<lgth1; i++ )
+	{
+		float maxpairscore = -9999.9;
+		float tmpscore;
+
+		for( j=0; j<lgth2; j++ )
+		{
+			if( maxpairscore < (tmpscore=WMMTX[i][j]) )
+			{
+				map12[i].pos = j;
+				map12[i].score = tmpscore;
+				maxpairscore = tmpscore;
+			}
+		}
+
+		for( k=0; k<lgth1; k++ )
+		{
+			if( i == k ) continue;
+			if( map12[i].score <= WMMTX[k][map12[i].pos] )
+				break;
+		}
+		if( k != lgth1 )
+		{
+			map12[i].pos = -1;
+			map12[i].score = -1.0;
+		}
+		fprintf( stderr, "pair of %d = %d (%f) %c:%c\n", i, map12[i].pos, map12[i].score, seq1[0][i], seq2[0][map12[i].pos] );
+	}
+	for( j=0; j<lgth2; j++ )
+	{
+		float maxpairscore = -9999.9;
+		float tmpscore;
+
+		for( i=0; i<lgth1; i++ )
+		{
+			if( maxpairscore < (tmpscore=WMMTX[i][j]) )
+			{
+				map21[j].pos = i;
+				map21[j].score = tmpscore;
+				maxpairscore = tmpscore;
+			}
+		}
+
+		for( k=0; k<lgth2; k++ )
+		{
+			if( j == k ) continue;
+			if( map21[j].score <= WMMTX[map21[j].pos][k] )
+				break;
+		}
+		if( k != lgth2 )
+		{
+			map21[j].pos = -1;
+			map21[j].score = -1.0;
+		}
+		fprintf( stderr, "pair of %d = %d (%f) %c:%c\n", j, map21[j].pos, map21[j].score, seq2[0][j], seq1[0][map21[j].pos] );
+	}
+
+	for( i=0; i<lgth1; i++ )
+	{
+		if( map12[i].pos != -1 ) if( map21[map12[i].pos].pos != i ) 
+			fprintf( stderr, "ERROR i=%d, but map12[i].pos=%d and map21[map12[i].pos]=%d\n", i, map12[i].pos, map21[map12[i].pos].pos );
+	}
+#endif
+
+#if 0
+	fprintf( stderr, "WMMTX = \n" );
+    for( i=0; i<lgth1; i++ )
+    {
+        fprintf( stderr, "%d ", i );
+        for( j=0; j<lgth2; j++ )
+        {
+            fprintf( stderr, "% 7.2f ", WMMTX[i][j] );
+        }
+        fprintf( stderr, "\n" );
+    }
+//	fprintf( stderr, "WMMTX2 = (p = %f)\n", fpenalty );
+    for( i=0; i<lgth1; i++ )
+    {
+        fprintf( stderr, "%d ", i );
+        for( j=0; j<lgth2+1; j++ )
+        {
+            fprintf( stderr, "% 7.2f ", WMMTX2[i][j] );
+        }
+        fprintf( stderr, "\n" );
+    }
+	exit( 1 );
+#endif
+
+#if 0
+    fprintf( stdout, "#WMMTX = \n" );
+    for( i=0; i<lgth1; i++ )
+    {
+//        fprintf( stdout, "%d ", i ); 
+        for( j=0; j<lgth2; j++ )
+        {
+//          if( WMMTX[i][j] > amino_dis['a']['g'] -1 )
+                fprintf( stdout, "%d %d %8.1f", i, j, WMMTX[i][j] );
+			if( WMMTX[i][j] == maxwm )
+                fprintf( stdout, "selected \n" );
+			else
+                fprintf( stdout, "\n" );
+        }
+        fprintf( stdout, "\n" );
+    }
+	exit( 1 );
+#endif
+
+#if 0
+
+	fprintf( stderr, "jumpbacki = \n" );
+	for( j=0; j<lgth2; j++ )
+	{
+		fprintf( stderr, "% 7d ", jumpbacki[j] );
+	}
+	fprintf( stderr, "\n" );
+	fprintf( stderr, "jumpbackj = \n" );
+	for( j=0; j<lgth2; j++ )
+	{
+		fprintf( stderr, "% 7d ", jumpbackj[j] );
+	}
+	fprintf( stderr, "\n" );
+	fprintf( stderr, "jumpforwi = \n" );
+	for( j=0; j<lgth2; j++ )
+	{
+		fprintf( stderr, "% 7d ", jumpforwi[j] );
+	}
+	fprintf( stderr, "\n" );
+	fprintf( stderr, "jumpforwj = \n" );
+	for( j=0; j<lgth2; j++ )
+	{
+		fprintf( stderr, "% 7d ", jumpforwj[j] );
+	}
+	fprintf( stderr, "\n" );
+#endif
+
+
+#endif
+
+
+//	Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );
+
+#if 0 // irukamo
+	resultlen = strlen( mseq1[0] );
+	if( alloclen < resultlen || resultlen > N )
+	{
+		fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
+		ErrorExit( "LENGTH OVER!\n" );
+	}
+#endif
+
+
+
+#if 0
+	fprintf( stderr, "jumpi = %d, imid = %d\n", jumpi, imid );
+	fprintf( stderr, "jumpj = %d, jmid = %d\n", jumpj, jmid );
+
+	fprintf( stderr, "imid = %d\n", imid );
+	fprintf( stderr, "jmid = %d\n", jmid );
+#endif
+
+
+	FreeFloatVec( w1 );
+	FreeFloatVec( w2 );
+	FreeFloatVec( initverticalw );
+	FreeFloatVec( lastverticalw );
+	FreeFloatVec( midw );
+	FreeFloatVec( midm );
+	FreeFloatVec( midn );
+
+	FreeIntVec( jumpbacki );
+	FreeIntVec( jumpbackj );
+	FreeIntVec( jumpforwi );
+	FreeIntVec( jumpforwj );
+	FreeIntVec( jumpdummi );
+	FreeIntVec( jumpdummj );
+
+	FreeFloatVec( m );
+	FreeIntVec( mp );
+
+	FreeFloatMtx( floatwork );
+	FreeIntMtx( intwork );
+
+#if STOREWM
+	FreeFloatMtx( WMMTX );
+	FreeFloatMtx( WMMTX2 );
+#endif
+
+
+	free( gaps );
+#if MEMSAVE
+	free( aseq1 );
+	free( aseq2 );
+#else
+	FreeCharMtx( aseq1 );
+	FreeCharMtx( aseq2 );
+#endif
+	
+	return( value );
+}
+
+
+
+float Lalignmm_hmout( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, char *sgap1, char *sgap2, char *egap1, char *egap2, float **map )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+//	int k;
+	int i, j;
+	int ll1, ll2;
+	int lgth1, lgth2;
+	float wm = 0.0;   /* int ?????? */
+	char **mseq1;
+	char **mseq2;
+//	char **mseq;
+	float *ogcp1;
+	float *ogcp2;
+	float *fgcp1;
+	float *fgcp2;
+	float **cpmx1;
+	float **cpmx2;
+	float **gapinfo;
+//	float fpenalty;
+	float fpenalty = (float)RNApenalty;
+	int nglen1, nglen2;
+
+
+
+
+
+#if 0
+	fprintf( stderr, "eff in SA+++align\n" );
+	for( i=0; i<icyc; i++ ) fprintf( stderr, "eff1[%d] = %f\n", i, eff1[i] );
+#endif
+
+	nglen1 = seqlen( seq1[0] );
+	nglen2 = seqlen( seq2[0] );
+
+	lgth1 = strlen( seq1[0] );
+	lgth2 = strlen( seq2[0] );
+
+	ll1 = ( (int)(lgth1) ) + 100;
+	ll2 = ( (int)(lgth2) ) + 100;
+
+	mseq1 = AllocateCharMtx( icyc, ll1+ll2 );
+	mseq2 = AllocateCharMtx( jcyc, ll1+ll2 );
+
+	gapinfo = AllocateFloatMtx( 4, 0 );
+	ogcp1 = AllocateFloatVec( ll1+2 );
+	ogcp2 = AllocateFloatVec( ll2+2 );
+	fgcp1 = AllocateFloatVec( ll1+2 );
+	fgcp2 = AllocateFloatVec( ll2+2 );
+
+
+	cpmx1 = AllocateFloatMtx( ll1+2, nalphabets+1 );
+	cpmx2 = AllocateFloatMtx( ll2+2, nalphabets+1 );
+
+	for( i=0; i<icyc; i++ ) 
+	{
+		if( strlen( seq1[i] ) != lgth1 )
+		{
+			fprintf( stderr, "i = %d / %d\n", i, icyc );
+			fprintf( stderr, "bug! hairetsu ga kowareta!\n" );
+			exit( 1 );
+		}
+	}
+	for( j=0; j<jcyc; j++ )
+	{
+		if( strlen( seq2[j] ) != lgth2 )
+		{
+			fprintf( stderr, "j = %d / %d\n", j, jcyc );
+			fprintf( stderr, "bug! hairetsu ga kowareta!\n" );
+			exit( 1 );
+		}
+	}
+
+	MScpmx_calc_new( seq1, cpmx1, eff1, lgth1, icyc );
+	MScpmx_calc_new( seq2, cpmx2, eff2, lgth2, jcyc );
+
+
+#if 1
+
+	if( sgap1 )
+	{
+		new_OpeningGapCount( ogcp1, icyc, seq1, eff1, lgth1, sgap1 );
+		new_OpeningGapCount( ogcp2, jcyc, seq2, eff2, lgth2, sgap2 );
+		new_FinalGapCount( fgcp1, icyc, seq1, eff1, lgth1, egap2 );
+		new_FinalGapCount( fgcp2, jcyc, seq2, eff2, lgth2, egap2 );
+	}
+	else
+	{
+		st_OpeningGapCount( ogcp1, icyc, seq1, eff1, lgth1 );
+		st_OpeningGapCount( ogcp2, jcyc, seq2, eff2, lgth2 );
+		st_FinalGapCount( fgcp1, icyc, seq1, eff1, lgth1 );
+		st_FinalGapCount( fgcp2, jcyc, seq2, eff2, lgth2 );
+	}
+
+#if 1
+	for( i=0; i<lgth1; i++ ) 
+	{
+		ogcp1[i] = 0.5 * ( 1.0 - ogcp1[i] ) * fpenalty;
+		fgcp1[i] = 0.5 * ( 1.0 - fgcp1[i] ) * fpenalty;
+//		fprintf( stderr, "fgcp1[%d] = %f\n", i, fgcp1[i] );
+	}
+	for( i=0; i<lgth2; i++ ) 
+	{
+		ogcp2[i] = 0.5 * ( 1.0 - ogcp2[i] ) * fpenalty;
+		fgcp2[i] = 0.5 * ( 1.0 - fgcp2[i] ) * fpenalty;
+//		fprintf( stderr, "fgcp2[%d] = %f\n", i, fgcp2[i] );
+	}
+#else
+	for( i=0; i<lgth1; i++ ) 
+	{
+		ogcp1[i] = 0.5 * fpenalty;
+		fgcp1[i] = 0.5 * fpenalty;
+	}
+	for( i=0; i<lgth2; i++ ) 
+	{
+		ogcp2[i] = 0.5 * fpenalty;
+		fgcp2[i] = 0.5 * fpenalty;
+	}
+#endif
+
+	gapinfo[0] = ogcp1;
+	gapinfo[1] = fgcp1;
+	gapinfo[2] = ogcp2;
+	gapinfo[3] = fgcp2;
+#endif
+
+#if 0
+	fprintf( stdout, "in MSalignmm.c\n" );
+	for( i=0; i<icyc; i++ )
+	{
+		fprintf( stdout, ">%d of GROUP1\n", i );
+		fprintf( stdout, "%s\n", seq1[i] );
+	}
+	for( i=0; i<jcyc; i++ )
+	{
+		fprintf( stdout, ">%d of GROUP2\n", i );
+		fprintf( stdout, "%s\n", seq2[i] );
+	}
+	fflush( stdout );
+#endif
+
+	wm = MSalignmm_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, 0, lgth1-1, 0, lgth2-1, alloclen, mseq1, mseq2, 0, gapinfo, map );
+#if DEBUG
+		fprintf( stderr, " seq1[0] = %s\n", seq1[0] );
+		fprintf( stderr, " seq2[0] = %s\n", seq2[0] );
+		fprintf( stderr, "mseq1[0] = %s\n", mseq1[0] );
+		fprintf( stderr, "mseq2[0] = %s\n", mseq2[0] );
+#endif
+
+//	fprintf( stderr, "wm = %f\n", wm );
+
+#if 0
+
+	for( i=0; i<icyc; i++ ) strcpy( seq1[i], mseq1[i] );
+	for( i=0; i<jcyc; i++ ) strcpy( seq2[i], mseq2[i] );
+
+	if( seqlen( seq1[0] ) != nglen1 )
+	{
+		fprintf( stderr, "bug! hairetsu ga kowareta! (nglen1) seqlen(seq1[0])=%d but nglen1=%d\n", seqlen( seq1[0] ), nglen1 );
+		fprintf( stderr, "seq1[0] = %s\n", seq1[0] );
+		exit( 1 );
+	}
+	if( seqlen( seq2[0] ) != nglen2 )
+	{
+		fprintf( stderr, "bug! hairetsu ga kowareta! (nglen2) seqlen(seq2[0])=%d but nglen2=%d\n", seqlen( seq2[0] ), nglen2 );
+		exit( 1 );
+	}
+#endif
+
+	FreeFloatVec( ogcp1 );
+	FreeFloatVec( ogcp2 );
+	FreeFloatVec( fgcp1 );
+	FreeFloatVec( fgcp2 );
+	FreeFloatMtx( cpmx1 );
+	FreeFloatMtx( cpmx2 );
+	free( (void *)gapinfo );
+
+	FreeCharMtx( mseq1 );
+	FreeCharMtx( mseq2 );
+
+	lgth1 = strlen( seq1[0] );
+	lgth2 = strlen( seq2[0] );
+	for( i=0; i<icyc; i++ ) 
+	{
+		if( strlen( seq1[i] ) != lgth1 )
+		{
+			fprintf( stderr, "i = %d / %d\n", i, icyc );
+			fprintf( stderr, "hairetsu ga kowareta (end of MSalignmm) !\n" );
+			exit( 1 );
+		}
+	}
+	for( j=0; j<jcyc; j++ )
+	{
+		if( strlen( seq2[j] ) != lgth2 )
+		{
+			fprintf( stderr, "j = %d / %d\n", j, jcyc );
+			fprintf( stderr, "hairetsu ga kowareta (end of MSalignmm) !\n" );
+			exit( 1 );
+		}
+	}
+
+	return( wm );
+}
+
+float Lalign2m2m_hmout( char **seq1, char **seq2, char **seq1r, char **seq2r, char *dir1, char *dir2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, char *sgap1, char *sgap2, char *egap1, char *egap2, float **map )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+//	int k;
+	int i, j;
+	int ll1, ll2;
+	int lgth1, lgth2;
+	float wm = 0.0;   /* int ?????? */
+	char **mseq1;
+	char **mseq2;
+	float *ogcp1;
+	float *ogcp2;
+	float *fgcp1;
+	float *fgcp2;
+	float **cpmx1;
+	float **cpmx2;
+	float **gapinfo;
+	float fpenalty = (float)penalty;
+	int nglen1, nglen2;
+
+#if 0
+	fprintf( stderr, "eff in SA+++align\n" );
+	for( i=0; i<icyc; i++ ) fprintf( stderr, "eff1[%d] = %f\n", i, eff1[i] );
+#endif
+
+	nglen1 = seqlen( seq1[0] );
+	nglen2 = seqlen( seq2[0] );
+
+	lgth1 = strlen( seq1[0] );
+	lgth2 = strlen( seq2[0] );
+
+	ll1 = ( (int)(lgth1) ) + 100;
+	ll2 = ( (int)(lgth2) ) + 100;
+
+	mseq1 = AllocateCharMtx( icyc, ll1+ll2 );
+	mseq2 = AllocateCharMtx( jcyc, ll1+ll2 );
+
+	gapinfo = AllocateFloatMtx( 4, 0 );
+	ogcp1 = AllocateFloatVec( ll1+2 );
+	ogcp2 = AllocateFloatVec( ll2+2 );
+	fgcp1 = AllocateFloatVec( ll1+2 );
+	fgcp2 = AllocateFloatVec( ll2+2 );
+
+
+	cpmx1 = AllocateFloatMtx( ll1+2, 39 );
+	cpmx2 = AllocateFloatMtx( ll2+2, 39 );
+
+	for( i=0; i<icyc; i++ ) 
+	{
+		if( strlen( seq1[i] ) != lgth1 )
+		{
+			fprintf( stderr, "i = %d / %d\n", i, icyc );
+			fprintf( stderr, "bug! hairetsu ga kowareta!\n" );
+			exit( 1 );
+		}
+	}
+	for( j=0; j<jcyc; j++ )
+	{
+		if( strlen( seq2[j] ) != lgth2 )
+		{
+			fprintf( stderr, "j = %d / %d\n", j, jcyc );
+			fprintf( stderr, "bug! hairetsu ga kowareta!\n" );
+			exit( 1 );
+		}
+	}
+
+#if 0
+	MScpmx_calc_new( seq1, cpmx1, eff1, lgth1, icyc );
+	MScpmx_calc_new( seq2, cpmx2, eff2, lgth2, jcyc );
+#else
+	cpmx_ribosum( seq1, seq1r, dir1, cpmx1, eff1, lgth1, icyc );
+	cpmx_ribosum( seq2, seq2r, dir2, cpmx2, eff2, lgth2, jcyc );
+#endif
+
+
+#if 1
+
+	if( sgap1 )
+	{
+		new_OpeningGapCount( ogcp1, icyc, seq1, eff1, lgth1, sgap1 );
+		new_OpeningGapCount( ogcp2, jcyc, seq2, eff2, lgth2, sgap2 );
+		new_FinalGapCount( fgcp1, icyc, seq1, eff1, lgth1, egap2 );
+		new_FinalGapCount( fgcp2, jcyc, seq2, eff2, lgth2, egap2 );
+	}
+	else
+	{
+		st_OpeningGapCount( ogcp1, icyc, seq1, eff1, lgth1 );
+		st_OpeningGapCount( ogcp2, jcyc, seq2, eff2, lgth2 );
+		st_FinalGapCount( fgcp1, icyc, seq1, eff1, lgth1 );
+		st_FinalGapCount( fgcp2, jcyc, seq2, eff2, lgth2 );
+	}
+
+#if 1
+	for( i=0; i<lgth1; i++ ) 
+	{
+		ogcp1[i] = 0.5 * ( 1.0 - ogcp1[i] ) * fpenalty;
+		fgcp1[i] = 0.5 * ( 1.0 - fgcp1[i] ) * fpenalty;
+//		fprintf( stderr, "fgcp1[%d] = %f\n", i, fgcp1[i] );
+	}
+	for( i=0; i<lgth2; i++ ) 
+	{
+		ogcp2[i] = 0.5 * ( 1.0 - ogcp2[i] ) * fpenalty;
+		fgcp2[i] = 0.5 * ( 1.0 - fgcp2[i] ) * fpenalty;
+//		fprintf( stderr, "fgcp2[%d] = %f\n", i, fgcp2[i] );
+	}
+#else
+	for( i=0; i<lgth1; i++ ) 
+	{
+		ogcp1[i] = 0.5 * fpenalty;
+		fgcp1[i] = 0.5 * fpenalty;
+	}
+	for( i=0; i<lgth2; i++ ) 
+	{
+		ogcp2[i] = 0.5 * fpenalty;
+		fgcp2[i] = 0.5 * fpenalty;
+	}
+#endif
+
+	gapinfo[0] = ogcp1;
+	gapinfo[1] = fgcp1;
+	gapinfo[2] = ogcp2;
+	gapinfo[3] = fgcp2;
+#endif
+
+#if 0
+	fprintf( stdout, "in MSalignmm.c\n" );
+	for( i=0; i<icyc; i++ )
+	{
+		fprintf( stdout, ">%d of GROUP1\n", i );
+		fprintf( stdout, "%s\n", seq1[i] );
+	}
+	for( i=0; i<jcyc; i++ )
+	{
+		fprintf( stdout, ">%d of GROUP2\n", i );
+		fprintf( stdout, "%s\n", seq2[i] );
+	}
+	fflush( stdout );
+#endif
+
+	wm = MSalign2m2m_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, 0, lgth1-1, 0, lgth2-1, alloclen, mseq1, mseq2, 0, gapinfo, map );
+#if DEBUG
+		fprintf( stderr, " seq1[0] = %s\n", seq1[0] );
+		fprintf( stderr, " seq2[0] = %s\n", seq2[0] );
+		fprintf( stderr, "mseq1[0] = %s\n", mseq1[0] );
+		fprintf( stderr, "mseq2[0] = %s\n", mseq2[0] );
+#endif
+
+//	fprintf( stderr, "wm = %f\n", wm );
+
+#if 0
+
+	for( i=0; i<icyc; i++ ) strcpy( seq1[i], mseq1[i] );
+	for( i=0; i<jcyc; i++ ) strcpy( seq2[i], mseq2[i] );
+
+	if( seqlen( seq1[0] ) != nglen1 )
+	{
+		fprintf( stderr, "bug! hairetsu ga kowareta! (nglen1) seqlen(seq1[0])=%d but nglen1=%d\n", seqlen( seq1[0] ), nglen1 );
+		fprintf( stderr, "seq1[0] = %s\n", seq1[0] );
+		exit( 1 );
+	}
+	if( seqlen( seq2[0] ) != nglen2 )
+	{
+		fprintf( stderr, "bug! hairetsu ga kowareta! (nglen2) seqlen(seq2[0])=%d but nglen2=%d\n", seqlen( seq2[0] ), nglen2 );
+		exit( 1 );
+	}
+#endif
+
+	FreeFloatVec( ogcp1 );
+	FreeFloatVec( ogcp2 );
+	FreeFloatVec( fgcp1 );
+	FreeFloatVec( fgcp2 );
+	FreeFloatMtx( cpmx1 );
+	FreeFloatMtx( cpmx2 );
+	free( (void *)gapinfo );
+
+	FreeCharMtx( mseq1 );
+	FreeCharMtx( mseq2 );
+
+	lgth1 = strlen( seq1[0] );
+	lgth2 = strlen( seq2[0] );
+	for( i=0; i<icyc; i++ ) 
+	{
+		if( strlen( seq1[i] ) != lgth1 )
+		{
+			fprintf( stderr, "i = %d / %d\n", i, icyc );
+			fprintf( stderr, "hairetsu ga kowareta (end of MSalignmm) !\n" );
+			exit( 1 );
+		}
+	}
+	for( j=0; j<jcyc; j++ )
+	{
+		if( strlen( seq2[j] ) != lgth2 )
+		{
+			fprintf( stderr, "j = %d / %d\n", j, jcyc );
+			fprintf( stderr, "hairetsu ga kowareta (end of MSalignmm) !\n" );
+			exit( 1 );
+		}
+	}
+
+	return( wm );
+}